ABSTRACT Pediatric HIV disease remains a great challenge globally, particularly in the developing world. Oral disorders cause significant morbidity and mortality in HIV-infected infants, children, and adults. Oral microbiota likely play a significant role in HIV disease-associated oral disorders. Further, pediatric HIV represents an excellent model system for the study of immunodeficiency-associated changes in oral microbiota because the disease is well- defined, with clearly established degrees of immune deficiency that are associated with significant clinical outcomes, and the abundant availability of a control group (healthy children and non-immune suppressed HIV- infected children). Pediatric HIV-associated oral disorders differ from those of adults, and the oral microbiota of children changes dramatically during development, due to the initial acquisition of oral flora by the uncolonized newborn, the changes in diet that accompany weaning and the adoption of an adult diet, and the development of dentition, from edentulous, to primary, mixed, and permanent dentition. Hence, any understanding of the involvement of the oral microbiota in the pathogenesis of HIV-associated oral disorders in children cannot rely on studies conducted in adults. We propose to assemble a cohort of HIV-infected children who are highly, moderately, and non- immune compromised who have primary, mixed, and permanent dentition, and a comparison cohort of normal children. Examining these cohorts, we will 1) Determine the species composition and rank abundance of the oral microbiota of a cohort of HIV-infected children with no/low, moderate, and severe degrees of immunosuppression and a normal control cohort using deep 16S rRNA gene analysis, 2) Determine the microbial community gene content (metagenome) and predicted metabolic capabilities of the oral microbiota of HIV-infected children and a normal control cohort using metagenomic shotgun sequencing, and 3) Determine the portfolio of expressed genes (metatranscriptome) of the oral microbiota of HIV-infected children and a normal control cohort. We will use the 454 pyrosequencing platform and a sophisticated bioinformatics and statistical analysis pipeline to study how the microbial community and community functional characteristics differ in immunosuppressed and non-immunosuppressed HIV-infected children and normal infected children and to understand how the functional abilities of the oral microbiota changes during development. The data obtained in the proposed study will provide key information to enable understanding of the influence of HIV-associated immunosuppression on the oral microbiota, the influence of immunosuppression generally on the oral microbiota, and the effects of dentition development on the microbiota. The information will be essential for the understanding of the pathogenesis of HIV-associated oral disorders. The data will also provide key insights into the development of the oral microbiota of normal children.